Open Research Projects, Research

Role of persistent herpesvirus in shaping innate immune clonality

Principle Investigator

Prof. Dr. Chiara Romagnani
Dr. Timo Rückert

Scientific interest within the context of the graduate college:

A hallmark of adaptive immunity is the clonal selection and expansion of cells with somatically diversified receptors and their long-term maintenance as memory cells. The innate immune system, in contrast, is wired to rapidly respond to pathogens via a broad set of germline-encoded receptors, acquiring epigenetic imprinting at the population level. One exception to this paradigm are Natural Killer (NK) cells, which can undergo specific expansion in response to murine and human Cytomegalovirus (CMV), raising conceptual parallels to adaptive immunity.1-3 In our more recent work, we have applied a single-cell multi-omic approach and leverage lineage tracing of human NK cells using mitochondrial mutations as endogenous barcodes4 to study clonality within the innate immune system and track NK cell memory to HCMV infection ex vivo. We have shown for the first time that HCMV induces the drastic expansion and differentiation of NK cell clones expressing the HCMV-specific receptor NKG2C,5 supporting a novel immunological paradigm of innate clonality.6

Project description:

Introduction: Based on this novel data, in this project we aim to investigate the dynamics of in vivo generation and maintenance of NK cell clonal expansions in response to primary HCMV infection.

To this aim, we will study NK cells isolated from HCMV- patients undergoing kidney transplantation from HCMV+ donors. These transplanted patients have a high risk of HCMV infection, which is regularly monitored in the clinic by measuring HCMV DNAemia and/or serology. Therefore this setting uniquely enables us to study the dynamics of primary HCMV infection, which is generally asymptomatic in healthy individuals. The cooperation with the nephrology clinic is already established, the ethical approval is already in place and prospective patient sample collection has already started. NK cells will be isolated from patient blood over time, i.e. between day 10 and day 30 after transplantation, during HCMV reactivation (typically around day 30) and at later time points (day 60-120). DOGMAseq, i.e. single-cell transcriptional, epigenetic, proteomic and lineage tracing analysis of NK cells will be performed, as previously published.5,7 The computational analysis of this large set of multiomic data will be performed using already established pipeline. Moreover, clinical and laboratory parameters along with sequencing of HCMV relevant proteins will be assessed. This project will uniquely provide an overview on the dynamics of innate clonality generation and maintenance in vivo and will enable the candidate to become familiar with important immunological and molecular biology technologies, such as flow cytometry and single-cell multiomc analysis as well as with bioinformatic analysis of data sets.


  1. Luetke-Eversloh M, Hammer Q, Durek P, Nordström K, Gasparoni G, Pink M, […], Chang HD, Dong J, Romagnani C. Human cytomegalovirus drives epigenetic imprinting of the IFNG locus in NKG2Chi natural killer cells. PLoS Pathog. 2014; 10(10):e1004441.
  2. Hammer Q, Rückert T, Borst EM, Dunst J, Haubner A, Durek P, […], Mashreghi MF, Messerle M, Romagnani C. Peptide-specific recognition of human cytomegalovirus strains controls adaptive natural killer cells. Nat Immunol. 2018; 19(5):453-463.
  3. Hammer Q, Rückert T, Romagnani C. Natural killer cell specificity for viral infections. Nat Immunol. 2018; 19(8):800-808.
  4. Ludwig LS, Lareau CA, Ulirsch JC, Christian E, Muus C, Li LH, […], Buenrostro JD, Regev A, Sankaran VG. Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics. Cell. 2019; 176(6):1325-1339.e22.
  5. Rückert T, Lareau CA, Mashreghi MF, Ludwig LS, Romagnani C. Clonal expansion and epigenetic inheritance of long-lasting NK cell memory. Nat Immunol. 2022; 23(11):1551-1563.
  6. Rückert T and Romagnani C. Extrinsic and intrinsic drivers of natural killer cell clonality. Immunol Rev. 2024; 323(1):80-106.
  7. Mimitou EP, Lareau CA, Chen KY, Zorzetto-Fernandes AL, Hao Y, Takeshima Y, […], Sankaran VG, Regev A, Smibert P. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells. Nat Biotechnol. 2021; 39(10):1246-1258.